Microarray genomotyping of key experimental strains of Neisseria gonorrhoeae reveals gene complement diversity and five new neisserial genes associated with Minimal Mobile Elements.

Using the Pan-Neisseria microarray, three commonly used gonococcal laboratory experimental strains were investigated (F62, MS11, & FA19). Genes absent from these strains, but present in strain FA1090, were assessed as is possible with typical microarrays. Due to the design of this microarray, additional genes were also identified. Differences were associated with Minimal Mobile Elements (MMEs) or known divergences. Genomotyping indicates the presence of genes previously only described in meningococci and shows the presence of the complete Gonococcal Genetic Island in N. gonorrhoeae strain FA19. Five new neisserial genes were identified through microarray genomotyping and subsequent sequencing of two divergent MMEs in N. gonorrhoeae strain MS11 and four MMEs in N. gonorrhoeae strain FA19. No differences were identified between N. gonorrhoeae strains FA1090 and F62, indicating that these strains are very similar.This study shows extensive similarity between the experimental strains, associated with a varying number of strain-specific genes. This provides a framework for those working with these strains to refer to the available gonococcal genome sequence, and is the first detailed comparison of gene complements between gonococcal strains.The Neisseria gonorrhoeae population structure is not clonal [1-5], its panmictic structure being the result of horizontal genetic exchange [6]. The pathogenic Neisseria spp. are naturally transformable [7] and chromosomal changes are largely mediated by homologous recombination. Natural competence for transformation and homologous recombination allow the generation of mosaic genes, such as the divergent opa genes [8,9], antigenic variation through recombination with silent cassettes, such as in the pilE/pilS system [10,11], and the horizontal exchange of whole genes or groups of genes in Minimal Mobile Elements (MMEs) [12]. A Minimal Mobile Element (MME) is defined as a region between two conserved genes within which different genes